So I waited to comment on this until I played the game for myself, and I feel the need to ask what, precisely, Joel and Ellie did that made Yhatzee dislike them so much.

I mean, it's implied that Joel has done some questionable things in the past by another character, but during the actual game, all he really does is defend himself. Up until the ending, at least, but his actions at the end of the game are understandable; not agreeable, mind, but totally within the realm of a normal human being.

And Ellie pretty much just defends herself too, but never crosses the moral event horizon like Joel arguably does.